{"id":"https://openalex.org/W4309097051","doi":"https://doi.org/10.1093/bioinformatics/btac738","title":"Achieving improved accuracy for imputation of ancient\u00a0DNA","display_name":"Achieving improved accuracy for imputation of ancient\u00a0DNA","publication_year":2022,"publication_date":"2022-11-15","ids":{"openalex":"https://openalex.org/W4309097051","doi":"https://doi.org/10.1093/bioinformatics/btac738","pmid":"https://pubmed.ncbi.nlm.nih.gov/36377787"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac738","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac738","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac738/48448843/btac738.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac738/48448843/btac738.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029611210","display_name":"Kristiina Ausmees","orcid":"https://orcid.org/0000-0002-6212-539X"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Kristiina Ausmees","raw_affiliation_strings":["Department of Information Technology, Uppsala University , Uppsala 751 05, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-6212-539X","affiliations":[{"raw_affiliation_string":"Department of Information Technology, Uppsala University , Uppsala 751 05, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065796691","display_name":"Carl Nettelblad","orcid":"https://orcid.org/0000-0003-0458-6902"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Carl Nettelblad","raw_affiliation_strings":["Department of Information Technology, Uppsala University , Uppsala 751 05, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-0458-6902","affiliations":[{"raw_affiliation_string":"Department of Information Technology, Uppsala University , Uppsala 751 05, Sweden","institution_ids":["https://openalex.org/I123387679"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5029611210","https://openalex.org/A5065796691"],"corresponding_institution_ids":["https://openalex.org/I123387679"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.5403,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.90268901,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.0015999999595806003,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12090","display_name":"Language and cultural evolution","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/3316","display_name":"Cultural Studies"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7624613642692566},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.6814844012260437},{"id":"https://openalex.org/keywords/ancient-dna","display_name":"Ancient DNA","score":0.6660246849060059},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6120598912239075},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5646199584007263},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.43988409638404846},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2510056495666504},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.22103923559188843},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.1490701138973236},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13419148325920105}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7624613642692566},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.6814844012260437},{"id":"https://openalex.org/C189338579","wikidata":"https://www.wikidata.org/wiki/Q290447","display_name":"Ancient DNA","level":3,"score":0.6660246849060059},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6120598912239075},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5646199584007263},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.43988409638404846},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2510056495666504},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.22103923559188843},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.1490701138973236},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13419148325920105},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005006","descriptor_name":"Ethnicity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005006","descriptor_name":"Ethnicity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005006","descriptor_name":"Ethnicity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac738","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac738","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac738/48448843/btac738.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36377787","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36377787","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:DiVA.org:uu-470292","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-470292","pdf_url":"https://uu.diva-portal.org/smash/get/diva2:1646316/FULLTEXT01","source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9805568","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805568","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac738","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac738","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac738/48448843/btac738.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4688730184","display_name":"Cost-effective genotyping in plant and animal breeding using computational analysis of pooled samples","funder_award_id":"2017-00453","funder_id":"https://openalex.org/F4320321033","funder_display_name":"Svenska Forskningsr\u00e5det Formas"}],"funders":[{"id":"https://openalex.org/F4320321033","display_name":"Svenska Forskningsr\u00e5det Formas","ror":"https://ror.org/03pjs1y45"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320336376","display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309097051.pdf","grobid_xml":"https://content.openalex.org/works/W4309097051.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1962960380","https://openalex.org/W1971635249","https://openalex.org/W1992436001","https://openalex.org/W2050967443","https://openalex.org/W2093478783","https://openalex.org/W2104549677","https://openalex.org/W2111307685","https://openalex.org/W2119180969","https://openalex.org/W2119279196","https://openalex.org/W2125838338","https://openalex.org/W2138345444","https://openalex.org/W2166501262","https://openalex.org/W2175307154","https://openalex.org/W2230276206","https://openalex.org/W2741074409","https://openalex.org/W2751146876","https://openalex.org/W2783113319","https://openalex.org/W2804307951","https://openalex.org/W2987060168","https://openalex.org/W3036347945","https://openalex.org/W3095727366","https://openalex.org/W3120295425","https://openalex.org/W4226172793","https://openalex.org/W4240204556"],"related_works":["https://openalex.org/W2055197888","https://openalex.org/W2056560357","https://openalex.org/W1965491053","https://openalex.org/W2000099891","https://openalex.org/W2052673034","https://openalex.org/W2057597395","https://openalex.org/W2022778960","https://openalex.org/W2389619865","https://openalex.org/W4211215373","https://openalex.org/W2411524895"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genotype":[1],"imputation":[2,58,92],"has":[3],"the":[4,8,17,46,62,76,103,109,132,168,187],"potential":[5],"to":[6,94,117,147],"increase":[7],"amount":[9],"of":[10,45,50,69],"information":[11,194],"that":[12,98,131],"can":[13],"be":[14,73],"gained":[15],"from":[16],"often":[18],"limited":[19],"biological":[20],"material":[21],"available":[22,185,196],"in":[23,37,48,102,158,186],"ancient":[24,51,81,104,114],"samples.":[25],"As":[26],"many":[27],"widely":[28],"used":[29,101],"tools":[30],"have":[31,99],"been":[32,100],"developed":[33],"with":[34,125],"modern":[35],"data":[36,115],"mind,":[38],"their":[39],"design":[40],"is":[41,135,154,184,195],"not":[42],"necessarily":[43],"reflective":[44],"requirements":[47],"studies":[49],"DNA.":[52],"Here,":[53],"we":[54,129],"investigate":[55],"if":[56],"an":[57,86],"method":[59,134],"based":[60,107],"on":[61,108,167,173],"full":[63],"probabilistic":[64],"Li":[65],"and":[66,90,145,163],"Stephens":[67],"model":[68],"haplotype":[70],"frequencies":[71],"might":[72],"beneficial":[74],"for":[75,156,182],"particular":[77],"challenges":[78],"posed":[79],"by":[80],"data.":[82],"RESULTS:":[83],"We":[84],"present":[85],"implementation":[87],"called":[88],"prophaser":[89,153,183],"compare":[91],"performance":[93],"two":[95],"alternative":[96],"pipelines":[97],"DNA":[105],"community":[106],"Beagle":[110],"software.":[111],"Considering":[112],"empirical":[113],"downsampled":[116],"lower":[118,138],"coverages":[119],"as":[120,122],"well":[121],"present-day":[123],"samples":[124],"artificially":[126],"thinned":[127],"genotypes,":[128],"show":[130],"proposed":[133],"advantageous":[136],"at":[137,197],"coverages,":[139],"where":[140],"it":[141],"yields":[142],"improved":[143],"accuracy":[144],"ability":[146],"capture":[148],"rare":[149],"variation.":[150],"The":[151,179],"software":[152],"optimized":[155],"running":[157],"a":[159,174],"massively":[160],"parallel":[161],"manner":[162],"achieved":[164],"reasonable":[165],"runtimes":[166],"experiments":[169],"performed":[170],"when":[171],"executed":[172],"GPU.":[175],"AVAILABILITY":[176],"AND":[177],"IMPLEMENTATION:":[178],"C++":[180],"code":[181],"GitHub":[188],"repository":[189],"https://github.com/scicompuu/prophaser.":[190],"SUPPLEMENTARY":[191],"INFORMATION:":[192],"Supplementary":[193],"Bioinformatics":[198],"online.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2025-10-10T00:00:00"}
